Olivier Tenaillon

Website: https://www.iame-research.center/eq1/research-interests/
ORCID: 0000-0002-3796-1601

With the rise of antibiotic resistance and the emergence of new forms of virulence, it has become clear that microbial evolution is at the heart of infectious diseases. The aim of our team is to study the microbial adaptation with a quantitative methodology.  For that purpose, we combine three approaches: experimental evolution, systems biology and population genetics/ comparative genomics.

Experimental evolution combined with whole genome sequencing allow us to uncover the molecular bases of adaptation in test tubes as well as in mice colonization models. Population genetics/Comparative genomics allow us to study rates and tempo of adaptation in the wild at different time scale: species wise, for a sequence type or within a host as commensal or pathogen and to compare the observed patterns with the ones derived from integrated models of adaptation, such as Fisher Geometric Model of Adaptation. Finally, we use systems biology approach, in which we study simulatenously thousands of mutants within small molecular systems (a gene, a small regularity network) to unravel the evolutionary and mechanistic constraints shaping the function of these molecular entities.

All these approaches take full benefit of the sequencing revolution, the computing progresses, as well as some high throughput phenotyping. Thanks to these technical advancements, we can increase both the level of replication and the description level of the clones and switch from a descriptive science to a quantitative one.

All the different facets of our expertise are used in the collaborative project DREAM, in which we will study the influence of human diet and host microbiota on the propagation of antibiotic resistance in our species of interest E. coli, using well characterized microbiota donors and artificial in vitro gut models.

2) We have a large expertise in molecular genetics, as well as sequence analysis from libraries of mutants to clones, populations as well as microbiota. We have an anaerobic hoot and a system allowing the maintenance of a microbiota over two weeks. A robotic platform of fluidic (TECAN EVOLUTION) and TECAN plate readers.

Top 5 publications

1. Vigué, G. Croce ,M. Petitjean,E. Ruppé, O. Tenaillon*, M. Weigt*: Deciphering polymorphism in 61,157 Escherichia coli genomes via epistatic sequence landscapes. Nature Communication, vol 13(1):4030, 2022. (*contribution egale)
2. Choudhury, J.A. Fenster, R.G. Fankhauser, J.L. Kaar, O. Tenaillon*, and R.T. Gill*: “CRISPR/Cas9 recombineering-mediated deep mutational scanning of essential genes in Escherichia coli.”Molecular Systems Bioliogyvol. 16, no. 3, pp. e9265, 2020. (*contribution egale)
3. Kemble, C. Eisenhauer, A. Couce, A. Chapron, M. Magnan, G. Gautier, H.L. Nagard, P. Nghe, and O. Tenaillon: “Flux, toxicity, and expression costs generate complex genetic interactions in a metabolic pathway.”Science Advancesvol. 6, no. 23, pp. eabb2236, 2020.
4. Lescat, A. Launay, M. Ghalayini, M. Magnan, J. Glodt, C. Pintard, S. Dion, E. Denamur, and O. Tenaillon: “Using long-term experimental evolution to uncover the patterns and determinants of molecular evolution of an Escherichia coli natural isolate in the streptomycin-treated mouse gut.”Molecular EcologyVol. 26 no. 7, pp 1082-1817, 2017.
5. Couce, L.V. Caudwell, C. Feinauer, T. Hindré, J.-P. Feugeas, M. Weigt, R.E. Lenski, D. Schneider, and O. Tenaillon: “Mutator genomes decay, despite sustained fitness gains, in a long-term experiment with bacteria.”Proc. Natl. Acad. Sci. vol. 114, no. 43, pp. E9026–E9035, 2017

Dernières publications sur HAL :